diff --git a/src/resources/extensions/gsd/auto-worktree.ts b/src/resources/extensions/gsd/auto-worktree.ts
index a0275619a..d2420257f 100644
--- a/src/resources/extensions/gsd/auto-worktree.ts
+++ b/src/resources/extensions/gsd/auto-worktree.ts
@@ -1453,8 +1453,13 @@ export function mergeMilestoneToMain(
     originalBasePath_,
     milestoneId,
   );
+  // Validate prefs.main_branch exists before using it — a stale preference
+  // (e.g. "master" when repo uses "main") causes merge failure (#3589).
+  const validatedPrefBranch = prefs.main_branch && nativeBranchExists(originalBasePath_, prefs.main_branch)
+    ? prefs.main_branch
+    : undefined;
   const mainBranch =
-    integrationBranch ?? prefs.main_branch ?? nativeDetectMainBranch(originalBasePath_);
+    integrationBranch ?? validatedPrefBranch ?? nativeDetectMainBranch(originalBasePath_);
 
   // Remove transient project-root state files before any branch or merge
   // operation. Untracked milestone metadata can otherwise block squash merges.
diff --git a/src/resources/extensions/gsd/commands/context.ts b/src/resources/extensions/gsd/commands/context.ts
index 7bbaa5790..f4a5aa423 100644
--- a/src/resources/extensions/gsd/commands/context.ts
+++ b/src/resources/extensions/gsd/commands/context.ts
@@ -13,7 +13,13 @@ export interface GsdDispatchContext {
 }
 
 export function projectRoot(): string {
-  const cwd = process.cwd();
+  let cwd: string;
+  try {
+    cwd = process.cwd();
+  } catch {
+    // cwd directory was deleted (e.g. worktree teardown) — fall back to HOME (#3598)
+    cwd = process.env.HOME ?? "/";
+  }
   const root = resolveProjectRoot(cwd);
   if (root !== cwd) {
     assertSafeDirectory(cwd);
diff --git a/src/resources/extensions/gsd/tests/project-root-cwd-crash.test.ts b/src/resources/extensions/gsd/tests/project-root-cwd-crash.test.ts
new file mode 100644
index 000000000..a75d3f13f
--- /dev/null
+++ b/src/resources/extensions/gsd/tests/project-root-cwd-crash.test.ts
@@ -0,0 +1,53 @@
+/**
+ * Regression test for #3598 — projectRoot ENOENT crash on deleted cwd
+ *
+ * When the working directory is deleted (e.g. worktree teardown), process.cwd()
+ * throws ENOENT. The fix wraps process.cwd() in a try/catch and falls back to
+ * process.env.HOME.
+ *
+ * Also verifies #3589 — nativeBranchExists validation for prefs.main_branch
+ * in auto-worktree.ts to prevent merge failures with stale preferences.
+ *
+ * Structural verification test — reads source to confirm the guards exist.
+ */
+
+import { describe, test } from 'node:test';
+import assert from 'node:assert/strict';
+import { readFileSync } from 'node:fs';
+import { fileURLToPath } from 'node:url';
+import { dirname, join } from 'node:path';
+
+const __filename = fileURLToPath(import.meta.url);
+const __dirname = dirname(__filename);
+
+const contextSource = readFileSync(join(__dirname, '..', 'commands', 'context.ts'), 'utf-8');
+const worktreeSource = readFileSync(join(__dirname, '..', 'auto-worktree.ts'), 'utf-8');
+
+describe('projectRoot cwd crash guard (#3598)', () => {
+  test('projectRoot wraps process.cwd() in try/catch', () => {
+    assert.match(contextSource, /try\s*\{[\s\S]*?process\.cwd\(\)/,
+      'process.cwd() should be inside a try block');
+  });
+
+  test('catch block falls back to process.env.HOME', () => {
+    assert.match(contextSource, /catch[\s\S]*?process\.env\.HOME/,
+      'catch block should fall back to process.env.HOME');
+  });
+
+  test('projectRoot function is exported', () => {
+    assert.match(contextSource, /export function projectRoot\(\)/,
+      'projectRoot should be an exported function');
+  });
+});
+
+describe('main_branch nativeBranchExists validation (#3589)', () => {
+  test('prefs.main_branch is validated with nativeBranchExists', () => {
+    assert.match(worktreeSource, /nativeBranchExists\(.*prefs\.main_branch\)/,
+      'nativeBranchExists should validate prefs.main_branch');
+  });
+
+  test('validatedPrefBranch falls back to undefined when branch missing', () => {
+    assert.match(worktreeSource, /validatedPrefBranch[\s\S]*?:\s*undefined/,
+      'validatedPrefBranch should fall back to undefined');
+  });
+});